Since 1968, Marteilia refringens bas caused serious and recurrent mortalities in the European flat oyster (Ostrea edulis) and continues nowadays to cause high mortalities in the Atlantic coast of France. Under the EEC Council directive 91/67 this parasite is included in list 2 of Annex A. This list includes serious pathogens causing important losses for the European shell aquaculture industry, that should be obligatory declared. An area where flat oysters or mussels are infected with any of these parasites will not be allowed to export to another area free of this disease. The diagnoses of the two species of Marteilia found in Europe (Marteilia refringens and Marteilia maurini) was done using ultrastructural characteristics and host specificity. However, it is not possible to establish whether one, two, or more species of Marteilia exist in bivalve molluscs in Europe. There is an urgent need to set up more sensitive and accurate methods to allow the detection of low prevalence of Marteilia and to clarify the taxonomy of this parasite. The existence of a complex life-cycle was early postulated by many authors. Because of the limitations of histology, a sensible and specific tool is needed to screen for Marteilia presence in intermediate or alternative hosts.